XLOC_003896 (lsm4)


Basic Information

Item Value
gene id XLOC_003896
gene name lsm4
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 6859876 ~ 6868474 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00007457
GGGACTTTTGCTTTGACAACTTCCGCTTTCACCTGGAAGTACAACAGTAAGTGGTTTGCAGATCGCCTTGTGCTGCGAAGAAGATTCACAGAAAATCATTTGTGATTGAAGTCTTCAGTGGATTAAAACTTCATATAAAGACTGATTGGTCATTCAGCTGACATGCTCCCGTTATCTTTACTGAAGACGGCACAGAACCACCCGATGCTGGTGGAGTTAAAGAATGGCGAGACATACAACGGCCATCTGGTCAGCTGCGACAACTGGATGAATATAAACTTGAGAGAAGTTATTTGCACTTCACGGGATGGAGATAAGTTTTGGAGGATGCCAGAATGCTACATAAGAGGAAGCACCATTAAATACTTGCGAATCCCTGATGAAATTATAGATATGGTGAAAGAGGAAGTGGTGTCAAAGGGCCGTGGCCGGGGTGGCATGCAGCAGAATAAGCCACAAGGAAAGGGCAGAGGAGGTGGACCTGGAAGAGGCGGCGGACCTGGCAGAGGTGTTTTTGGTGGCCGTGGCAGAGGCATGCAGGGATCTGGCCGTGGACAGCAACAAGACAAAAAGCCTGGAAAACAACAAGTTTGATCATCGACCAGAAAGAACGAGTTTAATTTGAAATGGACGTCCTGGATCTCCGTGAAGATTTTAATTTGGTGATGTTGATTTAAAGATGCTCTTTCATTCGttctaaactgttttattttgtcttcAGTCATTCGGTGCATGTTTTCACATTTCTCTTTTTGTGCTTTAAAACACAACCATGCTGTAAGTTTGACTTGTCTATATGCACTTGTGAATAAACGATTTTTGTTAAATATGG
>TCONS_00007458
gatgatgtgtggatgatttACACGgggcataactaagcaacacagcGATCTGTTAAGGAGGAAGTACTCCCGTTATCTTTACTGAAGACGGCACAGAACCACCCGATGCTGGTGGAGTTAAAGAATGGCGAGACATACAACGGCCATCTGGTCAGCTGCGACAACTGGATGAATATAAACTTGAGAGAAGTTATTTGCACTTCACGGGATGGAGATAAGTTTTGGAGGATGCCAGAATGCTACATAAGAGGAAGCACCATTAAATACTTGCGAATCCCTGATGAAATTATAGATATGGTGAAAGAGGAAGTGGTGTCAAAGGGCCGTGGCCGGGGTGGCATGCAGCAGAATAAGCCACAAGGAAAGGGCAGAGGAGGTGGACCTGGAAGAGGCGGCGGACCTGGCAGAGGTGTTTTTGGTGGCCGTGGCAGAGGCATGCAGGGATCTGGCCGTGGACAGCAACAAGACAAAAAGCCTGGAAAACAACAAGTTTGATCATCGACCAGAAAGAACGAGTTTAATTTGAAATGGACGTCCTGGATCTCCGTGAAGATTTTAATTTGGTGATGTTGATTTAAAGATGCTCTTTCATTCGttctaaactgttttattttgtcttcAGTCATTCGGTGCATGTTTTCACATTTCTCTTTTTGTGCTTTAAAACACAACCATGCTGTAAGTTTGACTTGTCTATATGCACTTGTGAATAAACGATTTTTGTTAAATATGG

Function

symbol description
lsm4 Predicted to enable U6 snRNA binding activity. Predicted to be involved in P-body assembly and spliceosomal snRNP assembly. Predicted to act upstream of or within mRNA splicing, via spliceosome and nuclear-transcribed mRNA catabolic process. Predicted to be located in nucleus. Predicted to be part of U6 snRNP and spliceosomal tri-snRNP complex. Predicted to be active in P-body. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated).

GO:

id name namespace
GO:0033962 P-body assembly biological_process
GO:0006396 RNA processing biological_process
GO:0006397 mRNA processing biological_process
GO:0000387 spliceosomal snRNP assembly biological_process
GO:0000398 mRNA splicing, via spliceosome biological_process
GO:0000956 nuclear-transcribed mRNA catabolic process biological_process
GO:0008380 RNA splicing biological_process
GO:0000932 P-body cellular_component
GO:0005634 nucleus cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005688 U6 snRNP cellular_component
GO:0097526 spliceosomal tri-snRNP complex cellular_component
GO:0017070 U6 snRNA binding molecular_function
GO:0003723 RNA binding molecular_function

KEGG:

id description
ko03040 Spliceosome
ko03018 RNA degradation
ko03019 Messenger RNA biogenesis
ko03041 Spliceosome

ZFIN:

id description
ZDB-GENE-040426-1652 Predicted to enable U6 snRNA binding activity. Predicted to be involved in P-body assembly and spliceosomal snRNP assembly. Predicted to act upstream of or within mRNA splicing, via spliceosome and nuclear-transcribed mRNA catabolic process. Predicted to be located in nucleus. Predicted to be part of U6 snRNP and spliceosomal tri-snRNP complex. Predicted to be active in P-body. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated).

Ensembl:

ensembl_id ENSDARG00000023852

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00007457 False 832 mRNA 0.43 6 6859876 6868287
TCONS_00007458 True 733 mRNA 0.44 6 6859876 6868474

Neighbor

gene id symbol gene type direction distance location
XLOC_003895 NA coding downstream 59938 6792546 ~ 6799938 (-)
XLOC_003894 BX936438.1 coding downstream 77800 6780708 ~ 6782076 (-)
XLOC_003893 NA coding downstream 403576 6455034 ~ 6456300 (-)
XLOC_003892 larp6b coding downstream 407384 6446235 ~ 6452492 (-)
XLOC_003891 NA coding downstream 428528 6429973 ~ 6431348 (-)
XLOC_003897 ddx49 coding upstream 838 6869312 ~ 6880725 (-)
XLOC_003898 comp coding upstream 72915 6941389 ~ 6974022 (-)
XLOC_003899 si:ch211-253b8.2 coding upstream 108794 6977268 ~ 6985463 (-)
XLOC_003900 zgc:173548 coding upstream 118115 6986589 ~ 6989598 (-)
XLOC_003901 cdh27 coding upstream 133474 7001948 ~ 7030047 (-)
XLOC_003938 BX324177.10 misc upstream 4470330 11338804 ~ 11339100 (-)
XLOC_003942 BX324177.17 misc upstream 4499120 11367594 ~ 11367890 (-)
XLOC_003943 BX324177.3 misc upstream 4501981 11370455 ~ 11370653 (-)
XLOC_003944 BX324177.4 misc upstream 4512430 11380904 ~ 11381204 (-)
XLOC_003945 BX324177.6 misc upstream 4515359 11383833 ~ 11384130 (-)
XLOC_003887 NA non-coding downstream 535319 6316654 ~ 6324557 (-)
XLOC_003904 CR925817.2 non-coding upstream 247773 7116247 ~ 7116363 (-)
XLOC_003908 NA non-coding upstream 477326 7345800 ~ 7349497 (-)
XLOC_003912 NA non-coding upstream 905358 7773832 ~ 7796332 (-)
XLOC_003920 CR847563.2 non-coding upstream 1608487 8476961 ~ 8515750 (-)
XLOC_003922 NA non-coding upstream 2115177 8983651 ~ 9523184 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) G245467 NA non-coding CI01000057 null 4455149 ~ 4457859 (+)
tiger barb (Puntius tetrazona) tomm7 NA misc NW_025048355.1 JAEQBD010000700.1 1536021 ~ 1541873 (+)